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International Conference on Combinatorial Optimization and Applications

COCOA 2017: Combinatorial Optimization and Applications pp 85–92Cite as

A New Approximation Algorithm for the Maximum Stacking Base Pairs Problem from RNA Secondary Structures Prediction

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 10627))

Abstract

This paper investigates the problem of maximum stacking base pairs from RNA secondary structure prediction. The basic version of maximum stacking base pairs problem as: given an RNA sequence, to find a maximum number of base pairs where each base pair is involved in a stacking. Ieong et al. showed this problem to be NP-hard, where the candidate base pairs follow some biology principle and are given implicitly. In this paper, we study the version of this problem that the candidate base pairs are given explicitly as input, and present a new approximation algorithm for this problem by the local search method, improving the approximation factor from 5/2 to 7/3. The time complexity is within \(O(n^{14})\), since we adopt 1-substitution and special 2-substitutions in the local improvement steps.

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Authors and Affiliations

  1. School of Computer Science and Technology and School of Mathematics and System Science, Shandong University, Jinan, People’s Republic of China

    Aizhong Zhou & Jiong Guo

  2. School of Computer Science and Technology, Shandong University, Jinan, People’s Republic of China

    Haitao Jiang & Daming Zhu

Authors
  1. Aizhong Zhou
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  2. Haitao Jiang
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  3. Jiong Guo
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  4. Daming Zhu
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Corresponding author

Correspondence to Haitao Jiang .

Editor information

Editors and Affiliations

  1. Shanghai Jiao Tong University, Shanghai, China

    Xiaofeng Gao

  2. Harbin Institute of Technology, Shenzhen, China

    Hongwei Du

  3. Kennesaw State University, Kennesaw, Georgia, USA

    Meng Han

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Zhou, A., Jiang, H., Guo, J., Zhu, D. (2017). A New Approximation Algorithm for the Maximum Stacking Base Pairs Problem from RNA Secondary Structures Prediction. In: Gao, X., Du, H., Han, M. (eds) Combinatorial Optimization and Applications. COCOA 2017. Lecture Notes in Computer Science(), vol 10627. Springer, Cham. https://doi.org/10.1007/978-3-319-71150-8_7

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  • DOI: https://doi.org/10.1007/978-3-319-71150-8_7

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-71149-2

  • Online ISBN: 978-3-319-71150-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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